Bioinformatics Workshop: Analysing PacBio Long-Read Data

Jointly organised by

In collaboration with PacBio and Genomics WA, we are holding a 2-day virtual workshop focusing on the applications of PacBio HiFi Data generated through the process of circular consensus sequences (CCS). Topics covered include using SMRT Link through the web GUI and on the command-line, CCS reads generation, de-novo assembly of long-reads and metagenomics applications.

This workshop will involve a mixture of presentations from the PacBio Team & hands-on activities.

Day 1 will begin with a 1.5 hour introduction to PacBio Sequencing & Genomics WA.
This session is open to all, free of charge to attend and no background technical knowledge is required.

After the introductory session, to allow for the most effective hands-on virtual training, the remainder of the event will be restricted to 30 participants and will cost $50 (excl. GST) to attend. Attendees are expected to be confident with the Linux command line and have prior experience with R/R studio.

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This workshop is supported by resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

Overview

Day 1 – Open Session

The starts with an open session introducing Genomics WA, PacBio HiFi Sequencing and Applications, and an overview of the SMRT Link software. This session is open to all, no prior knowledge or technical background required.

Day 1 – Workshop

After the open session the workshop starts, where participants will first explore the user-friendly software SMRT Link to generate CCS reads from raw subreads and analyze PacBio data, then dive deep into understanding the data structure of PacBio Data through the command line.

The day finishes with participants exploring the SMRT Link GUI on their own and becoming more experienced with the powerful analysis tools available by analysing some sample datasets in an advanced topics session, with opportunities to ask the PacBio experts questions.

Day 2 – Workshop (cont.)

On the second day, participants will learn how to perform de-novo WGS assembly from HiFi reads using a community tool. Then, the workshop will guide the participants to bring a set of 16S community data from FASTQ through to taxonomy assignment and visualization. The day ends with a continuation of day 1's advanced topics session to build on the skills learnt today, and closes after a Q&A session.

Workshop Requirements

A beginner or intermediate bioinformatician who can confidently use the linux/unix command line and with prior R/Rstudio experience.

We will provide a linux environment for workshop attendees, but you must be able to remotely login to the server using ssh and be able to use commands such as ls, screen, cd and nano on the command line.